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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCTTGCAGAAGTTCTCAgtatgtatccttgcctcactgacttaattgaaatattgtcaactgtattatttcccagtgtgttctttattccatggaatgggaattcctgtatctttaa...

Basic information

species Vitis vinifera
transcript Vv02s0012g01330.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G36700.2 (Glycine max), 5'ss of exon 5
GAAGTTCTCAaatgcaaaatctatctcatcagcccaatatttcggggatccgagtaaagccaatgacatggactctcaagtttccttgcagaagttctcagtatgtatccttgcctc-actgacttaattgaa-atattgtcaactgtattatttcccagtgtgttctttattccatggaatgggaattcctgtatctttaa
||||||||||||||| |||||||| || ||| |||||||||| || |||| ||  || ||    ||  |||| ||||||| | | |||   ||||| || ||||| |||||| |||  | | ||||  | ||| |||| ||   |      ||||       | ||   | ||| ||    ||     ||  |||       
GAAGTTCTCAAATGCTAAATCTATTTCTTCATCCCAATATTTTGGAGATCAGAACAAGGCTGCAGATGTGGATTCTCAAGCTACATTGTCTAAGTTTTCGgtatgcatcctttcctttaataacttgctggaacatatagtgtgcgaatacatttttgtagatcttggatgttcaatcccctgtattatcaagtaaaccc--
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110371364|gb|EC935333.1|EC935333
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|71867134|gb|DT016189.1|DT016189
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110405778|gb|EC971328.1|EC971328
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|33410214|gb|CF215841.1|CF215841
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|156736120|gb|EV240241.1|EV240241
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110380236|gb|EC945484.1|EC945484
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110400199|gb|EC966749.1|EC966749
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110364414|gb|EC924108.1|EC924108
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|45771808|gb|CN007660.1|CN007660
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|22011758|gb|BQ796792.1|BQ796792
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|30126699|gb|CB912038.1|CB912038
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110702022|gb|EE080258.1|EE080258
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|30128914|gb|CB914253.1|CB914253
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|30298086|gb|CB974880.1|CB974880
EST:     CGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCTTGCAGAAGTTCTCA                         GGTTCAACGGCCATATCAAGTGCTGATCTCTTTGGTCACAGTTCAGATAAT
genomic: CGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCTTGCAGAAGTTCTCAgtatgtatcc ... cctctcttagGGTTCAACGGCCATATCAAGTGCTGATCTCTTTGGTCACAGTTCAGATAAT
EST: gi|30127779|gb|CB913118.1|CB913118
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110702857|gb|EE079196.1|EE079196
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
EST: gi|110422737|gb|EC989065.1|EC989065
EST:     ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT
genomic: ATTGAGGAAAGTGATGAAGCTAGGAGGAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTTCTCAAATGCAAAATCTATCTCATCAGCCCAATATTTCGGGGATCCGAGTAAAGCCAATGACATGGACTCTCAAGTTTCCTTGCAGAAGTTCTCAgtatgtatccttgcctcactgacttaattgaaatattgtcaactgtattatttcccagtgtgttctttattccatggaatgggaattcctgtatctttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgggaa